Wed @ 11 meeting: Andrea - Sara-Ryan Lynn - Bob Steve Katie - Heidi Leslie Aleksi - Deborah
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Transcript of Wed @ 11 meeting: Andrea - Sara-Ryan Lynn - Bob Steve Katie - Heidi Leslie Aleksi - Deborah
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Wed @ 11 meeting:Andrea- Sara-RyanLynn - Bob SteveKatie- Heidi LeslieAleksi- DeborahEmily- Sarah JingTyler- Candice Jessica
Pics: homepage => Instructors
GradingMovie: BruceStuff => Tutorial Movies => ‘Grading Tao”
taProg: BruceStuff => TA Software
Must have VPN client running (available same page)
They (and you!) can see their grades from the homepage grade link
Master_of_Patterns; DNA walk-throughs posted
Emily will contact you about PMaster write-up conferences (guidance in rubric interpretation)
Expectations
Surface tension is a word.
“Billions of interlinings creating a tight mesh that doesn’t readily separate” is an explanation
It truly is exactly like popping the water balloon
stuff pulls back from the introduced point of weakness
See ‘TA_Guide’ for this type of walk through
Answers should be mechanistic, cause-effect!
Building Quizzes
See the QuizBank; it has examples and point distros
New as a 181L instructor? Please send your quiz draft to me 24-48 hours before you intend to distro
New
Party hats & replication, mutation demo
Desk drawing bases, charges
Paired homework
Nucleobases argument map (ID the claims & their support)
What is teaching?
How is it different from teaching a parrot to say words?
All the news that’s fit to print
A goes with TG goes with C
88
Spider dance!Spider dance!Now that’s ‘information’!Now that’s ‘information’!
99
DNA: instructions for the
parts of living things
DNA: instructions for the
parts of living things
Why the instructions for you are stored as hydrogen interactions between
ringy things
Why the instructions for you are stored as hydrogen interactions between
ringy things
How? Why?
10Who cares about DNA?• It’s what’s in you (and every other living thing)
• It’s (part of) the magical interface between chemistry and life
• It is perhaps the single most easily understood biomolecule you’ll ever meet
• doesn’t ‘do’ anything, its more or less inert
• key is in Hydrogen interaction pairing
• its structure IS its function
11
Use: GGGTT Green = GuanineRed = Cytosine
Blue = AdenineYellow = Thymine
1212
Primary goalsPrimary goalsConsider the necessary properties of a
chemical (DNA) that ‘is’ information
Understand HOW the bases go together
See how base pairing is replication
See how mutations arise
and why they cannot (always) be prevented
Genes in (in)action: genetic diseases
Consider the necessary properties of a chemical (DNA) that ‘is’ information
Understand HOW the bases go together
See how base pairing is replication
See how mutations arise
and why they cannot (always) be prevented
Genes in (in)action: genetic diseases
13Is today ‘science’?Are these
‘investigations’?• The goal of science is to create simplifying worldview
that is predictive and explanatory.
• We’re working with computers today: You’ll never feel the pull of electronegativity, the ‘pH-ey’ presence of a proton. But thinking in this way helps you explain, predict?
• That’s what we’re going for today in this way of looking at the bases
14
Life: gimme adjectives
What’s the difference between you, the bench top, a rock, a candle flame?
1515
Review: bonds and
“interactions”
Review: bonds and
“interactions”A few more pieces of reviewA few more pieces of review
16Four ‘bonds’/’interactions’
• Covalent: like a dowel. Arises from?
• Hydrogen interactions: like a wimpy old fridge magnet. Arises from?
• Hydrophobic interaction/exclusion: like nothing else. Arises from?
• Ionic: like a rare earth magnet. Arises from?
H-bond donors and acceptors
• Hydrogen interaction, H-bond: R-O-H - - - :N-R
• Donor (+): the group possessing the H, sharing it
• Acceptor (-): the partial (-) atom partaking of the H
17
19Which one of these is a part of the genetic code? Why
20Which one of these is a part of the genetic code? Why
Monomers Polymers Nucleotide Nucleic acid
Amino Acid Protein
21Building block
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Basil
Oregano
Salt
Garlic
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Adenine
Guanine
Cytosine
Thymine
24Blinding you with science (jargon)
• Pyrimidine (single ring), Purine (double)
• PUR As Gold
• Big base gets the little name
25
Use: GGGTT Green = GuanineRed = Cytosine
Blue = AdenineYellow = Thymine
26Pas de deux*
• Party hats on--we’re going to do some line dancing!
• Starting point: a double strand of DNA, each base facing partner with their ‘right hand’ on neighbor’s shoulder
• Each strand ‘count off’ from their L to R, how do the two directions compare?
• Separate strands; who partners with whom? What external info do we need to re-create the missing strand?
• Restart; ‘Mask’ one with a purple hat; it’s undergone chemical change
• replicate &…?
*Dictionary.com: a dance by two persons
Gua = GreenCyt = RedAde = BlueThy = Yellow
GGGTT
27
Fantastic plastic• Each group gets GC or AT pair. Investigate.
• Superimposability of GC, CG, AT, TA pairs
• High crimes & misdemeanors
28Anatomy of a basepair
H
Ornaments: -NH2=O-H-OH=NH
----- Dashed lines indicate double bonds present in some purines or pyrimidines
29
Hydrogen bonds form between G-C pairs and A-T pairs.
Guanine Cytosine
ThymineAdenine
Su
ga
r-p
ho
sp
ha
te b
ac
kb
on
e
Hydrogen bonds
DNA contains thymine,whereas RNA contains uracil
5′
5′3′
3′
Freeman, Biological Science, 4.6b
Text
Grow your own--make GC or AT
3030
Closer look:Pairing BasesCloser look:
Pairing Basesthe Truth about the Codethe Truth about the Code
31BasePairer
• Homepage = > my instructor link => this week => BasePairer rubric
• ‘Activity Guide’ is also on the web page
32
Basepairer• Launch ‘BasePairer’
• Don’t log in; that’s for homework
• Write your names on the paper I hand out; return it at end of class or zero credit
• make a note of your group name & genetic disease in your lab notebook
DNA
• What properties of DNA…
• Make it a good molecule to store info?
• Make it easy to copy?
33
34Precision & Pickiness
• H-bonds: because weak, picky
• Combined with stiff bases: it’s all right or it it’s wrong
35Chemistry Happens II• Dr. Base & Mr. Tautomer
• Why Chargaff’s rules didn’t => the structure
%A%A %T%T %G%G %C%C
MycobacteriumMycobacterium 15.1 14.6 34.9 35.4
YeastYeast 31.3 32.9 18.7 17.1
WheatWheat 27.3 27.1 22.7 22.8
Sea UrchinSea Urchin 32.8 32.1 17.7 17.3
Marine CrabMarine Crab 47.3 47.3 2.7 2.7
TurtleTurtle 29.7 27.9 22 21.3
RatRat 28.6 28.4 21.4 21.5
HumanHuman 30.9 29.4 19.9 19.8
36
http://www.nature.com/scitable/nated/content/ne0000/ne0000/ne0000/ne0000/97271/pierce_17_11_FULL.jpg
Stuff happens (baaaad stuff)
Bad things happen to good bases
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Deamination
Cytosine
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
DeAMINation
Cytosine
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Deamination
Cytosine
just add water…and heat
H2
O
NH3
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Deamination
Cytosine
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Deamination
Cytosine
Hmmm, this is IDENTICAL to THIS
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Deamination
Cytosine
We started with Cytosine
Deaminated it to
URACIL
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Deamination
CytosineUracil
Thymine
4545
Genetic DiseasesGenetic DiseasesWhy mutations matter
What loss of genetic information looks likeWhy mutations matter
What loss of genetic information looks like
46
This exercise...• Spans the next month – same groups all month!
• Lets you apply your learning and thinking to an actual disease
• What is most important is that you think well and integrate what you are learning; being ‘right’ is secondary
47The task
• Over the coming weeks, you’ll characterize a genetic disease
• Symptoms and distribution (DUE AT END OF THIS LAB!)
• DNA mutation, amino acid change
• Your ideas about influence on protein structure
• Then you’ll share your findings with the class
48Google & WikipediaGoogle & Wikipedia
• GOOGLE.com (or Blackle.com)
• search several terms
• “phrases in quotes”
• google.com/advanced_search
• Wikipedia.org
• User contributed
• User policed
• But pretty good! If you want to Bing, I’m not stopping you
Caveat emptor! The web is a wonderful, rich source of
information. ***But anybody can have a
webpage***
49My sources
• Wikipedia: I generally trust it based on personal experience and b/c it is community edited and putting up lies about science just isn’t that interesting
• NIH: Federally funded science & health professionals, I judge it generally very trustworthy
• Campbell textbook: textbook authors are not experts in every area of content, they consult with experts and their work is critically read by thousands, so I trust it
50Due today!• Genetic disease part 1, from today on calendar
• Handed in to me with all group member names on it
• An example:
hemoglobin/sickle cell anemia
• Sufferers: one in 12 African Americans has the TRAIT; overall, 1/5000 Americans suffer
• Common in areas with malaria
• symptoms: shortened lifespan (48-52), see next slide”
Homework 51
5252HomeworkHomeworkVocab: Transcription & Translation words
Assessor: Examining DNA/Introducing translationAssessor: Solving the Structure (remember your
tautomer)Basepairer as individual or pair
READ LAB 4!!!*
Turn in your Mix and Match Liquids lab in my TA dropbox Bio Sci East rm. 109
Vocab: Transcription & Translation wordsAssessor: Examining DNA/Introducing translationAssessor: Solving the Structure (remember your
tautomer)Basepairer as individual or pair
READ LAB 4!!!*
Turn in your Mix and Match Liquids lab in my TA dropbox Bio Sci East rm. 109
*Next week’s quiz emphasizesQuestions from the manual reading
Grading BasePairer
How the grading software works: UberPlayer
Movie: ‘Grading BasePairer
Entering grades: taProg
5454
HonorsHonorsDeaminationDeamination
55Things left out in water
and oxygen)
http://simple.wikipedia.org/wiki/File:Rust.rost.JPG
http://upload.wikimedia.org/wikipedia/commons/6/6e/Statue_of_Liberty_frontal_2.jpg
5656
Old walk-thruOld walk-thru
TA note
Following slides are old version to help you stay organized
They exactly parallel the instructions now linked from assignment & software calendars
Alert! Added ability to store A:C pair after manual printing, so it’s in instructions, but not in the manual version of the rubric
58BasePairer
Choose Guanine. Leave it be.
Describe it’s ‘pairing positions’
Deduce the face of its partner
On the right, select Cytosine
Analyze
Execute! (keep track of movements [watch the big letter ‘C ’)
Record
Turn on ‘show backbone’
59
Repeat with AT
60
Crosswise pairing
What can you do with G-T, A-C (antiparallel, 3-aligned)
Record it when you get it
Consider codes. How does it work with ‘pick your partner?
STOP!
Whatever you are doing, ask
What challenges might students be encountering with the software here?
...with the concepts?
How will you answer questions they ask you?
62Uh-oh
Click ‘Just look’ checkbox so it is on/checked
Pull up Adenine on the left; Hypoxanthine right
What’s the difference?
Consequences: go back to ‘Examine pairs’
Now look at Hypoxanthine:Cytosine
Record it
6363
Old: The wetstuffOld: The wetstuffDNA: Is it in you?DNA: Is it in you?
6464
Old/unusedOld/unused
65Sense-making
http://dd.dynamicdiagrams.com/wp-content/uploads/2011/01/orrery_2006.swf
created by Piotr Kaczmarek
66
“Nowhere is there anything resembling a blueprint of the body. At most, the genome is a set of instructions for making a body: it is not a description of a body.”
The Major Transitions in Evolution, J. M. Smith & E. Szathmary p. 257
6767
Implications & Uses
Implications & Uses
68Copying: easy as falling down
• Note that A & T; G & C ‘know’ each other by touch
• No machine needs (or uses) a ‘dictionary’ to pair them; only needs to know when a partner has been found for whatever is already there
• DNA Polymerase (the copy-maker!) indeed has no great attachment to A, T, G, C; can work with others if they H-bond*
The Examining DNA assessment will display some basepairs NOT found in our genetic code that can nonetheless be copied with good fidelity by some DNA polymerases--it’s the match, not the participants
69Ending notes
• Polymerase Chain Reaction
• Picky Pairing of short DNA strands
• the Rest is Replication
• Sensitivity: who smoked that cigarette?
• The PCR song (Bio-Rad)
70
How is RNA different from DNA?
Two, maybe 3 reasons
7171
DNA toysDNA toys
72Fun with basepairing
73
How does this work?http://www.sciencedaily.com/releases/2009/04/090402143507.htm
Movie in TA desktop folder
7474
Rube Goldberg in your genome
Rube Goldberg in your genome
The twisted tail of the ‘innovation’ of thymine from the ground state of uracil
The twisted tail of the ‘innovation’ of thymine from the ground state of uracil
75What’s the big deal?
76
What’s up with U?• Just a T without the -CH3
• In terms of basepairing, identical in the partnering with A
• Historically, U came first (as RNA preceded DNA); FYI, the ‘marking’ of T allows better maintenance/repair of DNA than is available in RNA
7777
My older, more extensive code
stuff
My older, more extensive code
stuff
78Information and Copying
• Morse code: .... . ._.. ._.. _ _ _
• English: Hello
• French: Bonjour
• Chinese
• Arabic
http://www.chinese-symbols.com/h-chinese-symbol-for-hello
http://members.virtualtourist.com/m/9cfaf/1c5710/a/
Chinese, Arabic contr. by Libby Landeen
79
Making copiesImagine a two-part machine--one part sees/feels the old, one generates the new. Verbalize the minimum instruction set (terms) needed to transcribe*...
Morse?
English?
Chinese?
Example: English
E: make vertical line. Make half-length horizontal lines from top, middle and bottom of vertical line, with one endpoint on the vertical line and extending to the right
Q: ???
*A term we’ll see again; lit. “write across”
80Nitrogen-containing bases
Cytosine (C) Uracil (U)
Pyrimidines
Thymine (T)
Guanine (G) Adenine (A)
Purines
Freeman, Biological Science, 4.1
81Hydrogen bonds form between G-C pairs and A-T pairs.
Guanine Cytosine
ThymineAdenineS
ug
ar-
ph
os
ph
ate
ba
ck
bo
ne
Hydrogen bonds
DNA contains thymine,whereas RNA contains uracil
5′
5′3′
3′
Freeman, Biological Science, 4.6b
82
Printing pressesImagine you had a 3D (think braille) representation of a message
If you pressed clay over it, what kind of ‘copy’ would you get?
What process would you need to make a duplicate of the original?
83
ExamplesHow many ‘binary copy systems’* can you think of in the macro world?
snaps on jeans
*If you could only do things by feel, you could take an existing string and partner each element with another element that somehow ‘matched’ it
84
• Adenine: from the Greek word for gland
• Thymine: first isolated from the thymus
• Cytosine isolated from ‘cells’ (think cytoplasm)
• Guanine: Yep--first isolated from bird guano
Why do we call them that?